It's not my theory. It's the normal ToE. I suggest reading up on that if you want to find out about mutations.

If you are relying on mutations to solve your evolutionary dilemmas, this doesn't help with the problem given. A mutant gene, as in the example given, leaves no indication of ancestry or lineage. P, Q, and R, in the example, offer no trace as to who the parent was. Was it a fish, was it a bird was it a plane? Dunno....

If you are relying on mutations to solve your evolutionary dilemmas, this doesn't help with the problem given. A mutant gene, as in the example given, leaves no indication of ancestry or lineage. P, Q, and R, in the example, offer no trace as to who the parent was. Was it a fish, was it a bird was it a plane? Dunno....

No they're not, you said so yourself in the example. A, B and C all have the X,Y and Z genes, as do all the rabits.

We know that some modern fish have X,Y,Z. These will have mated with fish which don't have X,Y,Z. (As in B or C's mate.) Most common ancestors therefore are unlikely to have X,Y,Z. We cannot therefore use X,Y,Z to determine lineage.

We know that some modern fish have X,Y,Z. These will have mated with fish which don't have X,Y,Z. (As in B or C's mate.)

So? You said there were modern fish with X, Y and Z, (the descendants of B) and also that all rabits had X, Y and Z (The descendants of C). This means that if they have a common ancestor, which they do, it should also have genes X, Y and Z. in your example this would be A and in your example it has those genes.

Most common ancestors therefore are unlikely to have X,Y,Z. We cannot therefore use X,Y,Z to determine lineage.

Of course we can, the common ancestor should have those genes. And in your example (A) was the common ancestor and has those genes. Or have you forgotten your own example?

The traditional definition of species is as a group of organisms capable of interbreeding and producing fertile offspring. Advances in genetics could offer a more precise genome sequenced definition of species. Segments of the genome could be used to define existing species and assist in identifying new species.

This might be an arbitrary system but it would be far more accurate and effective amongst known living species. eg no one would doubt that a polar bear and a brown bear are different species but they can interbreed and produce fertile offspring. The genome sequencing definition of species would allow us to identify the species, the hybrid, parentage and lineage. Hence this system has to be the preferred system of definition in the modern age.

In the previous comments we had the example that P,Q,R makes a rabbit a rabbit. No other species would contain P,Q,R because if it did it would be a rabbit. Thus we could use the genome sequence of P,Q,R to define a rabbit. This however, does not help us with history. If the rabbits had evolved from a rabbit like creature then this system of defining species would start to come into question. A rabbit like creature might contain say P,Q only. If on the other hand we follow the ID philosophy we can adopt the like begats like ideology. eg P,Q,R always leads to P,Q,R except in the case of tragic abnormalities and mutants.

The traditional definition of species is as a group of organisms capable of interbreeding and producing fertile offspring.

Actually, the even more traditional definition of species is as a group of organisms that possesses a given list of characteristics, which is pretty much what you're advocating here (although you are using genetic characters, whereas classical taxonomists used morphological characters). This is called ďtaxonomy.Ē The only difference is that you want species identification to require lots of expensive, fancy equipment.

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Big_Al35 writes:

Segments of the genome could be used to define existing species and assist in identifying new species.

This might be an arbitrary system but it would be far more accurate and effective amongst known living species...

... Hence this system has to be the preferred system of definition in the modern age.

So, basically, you want species definitions to just be an academic exercise of assigning names to things, and donít really care whether it has meaning in the biological world or benefit to people who donít have the expertise, equipment and funding to sequence genomes?

Fascinating.

I argue that the only reason to use the methodology you espouse is because it satisfyingly parcels things into convenient packages of information that sound nice to you. But, it isnít any more accurate or correct than any other proposed methodology, and it severely restricts the number of people who can do it.

The reason the ďbiological speciesĒ concept (the interbreeding criterion) was developed was to give taxonomy a reasonable grounding in reality. If we define two species based on differences in characteristics (be they molecular or morphological), then find that these differences have virtually no effect on how these organisms interact with one another, what, exactly, is the point of defining them as two species? The satisfaction of a tidy output? The solving of a little puzzle?

Classification does not exist just for the sake of classifying organisms: It exists to help scientists organize information about organisms in ways that are meaningful to the study of organisms.

Donít get me wrong: there is some meaningful information about the process of evolution that can be gleaned from your proposed methodology (and thatís why many people subscribe to it), but thatís the extent of its usefulness, and gleaning that information doesn't ever require naming and defining species, anyway.

The traditional definition of species is as a group of organisms capable of interbreeding and producing fertile offspring.

No, no, no! A thousand times no!

That's the Biological Species Concept, it's not even close to the traditional definition of a species - dating back only to the middle of the last century. Two hundred years after Linnaeus, yet alone the notion of a species! It's also not a great definition of species anyway.

I've written at length previously about the problems with it. I'll reproduce that post here, to save you clicking a link:

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The problem of species

The concept of a species predates Linnaeus, as does binomial naming, but he was he who formalised them and grouped them into Genera, Families, etc. in the familiar system that we still use today. Unfortunately, this system was defined before microscopy, before Darwin's theory of evolution, before Watson and Crick's discovery of DNA and otherwise before the rise of modern biology. It is concept from an age when it was thought that species were the eternal, unchanging creations of God.

We continue to use it because having a grouping for very similar organisms is useful in all sorts of ways and many, many attempts have been made to formalise the concept. They've all failed. The most successful is the Biological Species Concept (BSC), which was originally formulated as "are the same species if they can produce fertile offspring" but later modified to "do so in the wild"1. The BSC has proved an extremely powerful tool for distinguishing species - so much so that many people think it is the definition of species - but it can only be applied to a tiny proportion of currently living organisms.

The vast majority of reproduction on this planet is asexual: all bacteria and all archaea reproduce this way (and just to make things worse they go in for large amounts of horizontal gene transfer) then there's the many eukaryotes that reproduce asexually, both single cellular and multicellular. If things don't reproduce sexually, then the BSC simply can't be applied to them. Most things that have ever lived are now dead, and worse most types of things that have ever lived are now dead. There are countless species that we only known from the fossil record. The BSC cannot be applied to any of the species, because we have no way of telling what they could or couldn't breed with.

So having ruled out the extinct and the asexual, we're left with a small portion of the things we'd like to group into species, probably less than a hundredth of one percent of all living things. But, hey, these species include the big, familiar stuff so that's okay, right? Well.. kinda. Even among the organisms we're familiar with the BSC is hard to apply - you can't, for example, define something as a new species based on a few dead examples or a bit of videos you need to study live specimens in the field, or better yet gene screen a goodly sample - and doesn't actually work all that well anyway. Plants, especially, are particularly fond of forming viable hybrids with different populations we'd really like to describe as different species, and even among the animals creatures like butterflies are alarming fond of merrily hybridising away.

And then you get the crazy edge case hybrids, fish like Poeciliopsis monacha-lucida which is formed by hybridisation of a female P. monacha and a male P. lucida. P. monacha-lucida can viably breed with male P. Lucida but no crossing over occurs, instead the offspring inherit their maternal genome exactly as passed down from the P. monacha, freshly combined with the new chromosomes from the P. lucida sperm. Even whackier is the Amazon molly Poecilia formosa, formed by hybridisation of P. latipinna and P. mexicana. It has to mate with a male Poecilia sp. but the genetic material from that "father" is entirely discarded and the offspring is a genetic clone of the mother. Are these separate species? If not, which species are they? Are they truly a viable hybrid with their crazy forms of reproduction2?

I've concentrated on the BSC here, because it's the idea most commonly advanced as the species definition but I assure that all the other ideas for a definition have suffered from a similar array of problems. There just isn't a single, universally applicable definition of species; instead what is called a species is worked out by on an ad hoc basis by the scientists working in the field using an array of different and varied tools and a great deal of debate. This is particularly true for prokaryotes and fossil species.

To me, this is not surprising, because as I alluded to in my introduction, the concept of a species predates modern biology. The simple fact is that in the light of evolutionary understanding the concept of species is a shaky one as best, perhaps applicable if you view a single snapshot of time, but fundamentally flawed on a longer timescale. The features of organisms within a population change over time (as their genes change), in a way that means that had you a perfect record of these organisms lined up in temporal order it would not be possible for you to point to a particular point where they changed from one species to another but if you looked at the ends of the line you'd find two very different organisms. It is this continuity that makes dividing organisms into discrete species a flawed concept3.

So, in my view, species should not be viewed as a real division of organisms but rather as an idealised tool for understanding the diversity of organisms.

1 - The Biological Species Concept can be defined extremely formally and precisely in terms of gene flow but I think that's a needless complication here.2 - If anyone's interested these two forms of reproduction are called hydridogenesis and gynogenesis, respectively.3 - The same problem occurs on a smaller scale with ring species.

To me, this is not surprising, because as I alluded to in my introduction, the concept of a species predates modern biology. The simple fact is that in the light of evolutionary understanding the concept of species is a shaky one as best, perhaps applicable if you view a single snapshot of time, but fundamentally flawed on a longer timescale.

Earlier in this debate...see the off topic posts after message 87....we kind of established that the ancestors of modern fish were infact ancient fish. This idea that the usual definitions of species can't be applied in this case are therefore simply not true. I am suggesting that the normal definitions of species ie (similar behaviour, type etc and interbreeding and possibly even DNA) are still useful in this case and no snapshot in time is required.

Other cases we can debate but this is one case where any definition of species would be adequate. We are even using the term fish for the ancient fish and not some other word. That in itself is a clue.

Ofcourse we don't have access to ancient DNA and therefore the newer models for species definition have limited applicability. This might change with advances in technology.

"Fish" is not a species. "Fish" is not even a genus, a family, an order, a class or a phylum. (And "Fish" is certainly not a clade!)

So I'm not sure why you think the fact that ancient fish were also fish is particularly relevant to the question about species.

I am suggesting that the normal definitions of species ie (similar behaviour, type etc and interbreeding and possibly even DNA) are still useful in this case and no snapshot in time is required.

It's your idea that there's a "normal definition" of species I'm objecting to. There isn't. It's not a well defined concept. However, it is a useful one and, I would argue, the best way to apply it is to employ a holistic approach that adopts the various techniques at our disposal so while interbreeding is useful for some, for fossils it has no value, and while morphology is difficult to apply to others, for fossils it's the best (and often only) methodology available to us.